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Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-mediated Activation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 291 28% PEG4000, 0.1 M MMT, 0.2 M ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.91 35.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.982 α = 90 b = 41.481 β = 90 c = 91.663 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker Platinum 135 2011-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 27.13 96 0.087 13.8 14390 13808 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 39.8 0.098 7 1.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 4EPV 1.801 27.13 1.34 14390 13753 690 95.96 0.1625 0.1606 0.1575 0.1991 0.1971
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -3.196 2.5412 0.6548
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.672 f_angle_d 0.829 f_chiral_restr 0.053 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1358 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 56
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling